Description

Repeat Masker track constructed with the HMMER alignment engine and Dfam_3.1 database.

Display Conventions and Configuration

Color is based on repeat name or family:

RepeatColorRepeatColor
(CATTC)n (GAATC)n
ALR/Alpha BSR/Beta
CER DNA
GSAT HSAT
LINE Low_complexity
LSAU LTR
RC/Helitron Retroposon
RNA rRNA
SAR Satellite/acro
Satellite/telo SATR1
scRNA Simple repeat
SINE snRNA
srpRNA SSTI
SUBTEL_sa tRNA
Unknown

Methods

RepeatMasker with Dfam.

Credits

Thanks to Arian Smit, Robert Hubley, and the Dfam project for providing the tools and models used to generate this track.

References

Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010.

Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846

Robert Hubley; Robert D. Finn; Jody Clements; Sean R. Eddy; Thomas A. Jones; Weidong Bao; Arian F.A. Smit; Travis J. Wheeler The Dfam database of repetitive DNA families Nucleic Acids Research (2016) Database Issue 44:D81-89. DOI: 10.1093/nar/gkv1272

For a discussion of repeats in mammalian genomes, see:

Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):657-63. PMID: 10607616